The present invention generally relates to the field of nucleic acid chemistry. More specifically, the invention relates to a method of using PCR amplification to determine haplotypes.
Genetic research has shown that an individual's disease, risk of disease and response to therapeutic treatment is determined by variants or polymorphisms (alleles) in a gene at a particular genetic locus or in some cases at multiple genetic loci. The particular combination of genetic polymorphisms at multiple loci is referred to as the “haplotype”. Identification and characterization of such polymorphisms, particularly haplotypes, has therefore become a primary focus of genetic research.
In order to map disease genes and establish founder effects attributable to haplotypes, it is necessary to determine whether or not polymorphisms at multiple genetic loci are present on the same chromosome (the linkage phase). Eukaryotes, such as human, animals and plants, contain two copies of each gene, one on each of two chromosomes inherited from a parent (with the exceptions that the male X and Y chromosomes contain only a single copy of genes, and mitochondrial DNA is present as maternally inherited copies. Frequently, these two copies contain differences in the DNA sequence, attributable to mutations or recombination events, which may increase the risk of or cause a disease, or may render an individual more or less responsive to drug treatment. If a particular mutation in a gene is present on one of the genes but not the other, the gene is said to be heterozygous for that mutation. If both genes have the same mutation, the mutation is homozygous. Certain diseases are manifest only if a gene has multiple mutations at different locations on the same gene (the mutations are in cis phase), while the disease is not manifest if the same mutations are present but on different chromosomes (the mutations are in trans phase). Vice versa, disease can be associated with the trans phase on two mutations while the non-disease status is associated with the cis phase In the event that a gene is determined to have polymorphisms at multiple genetic loci, it is often difficult to determine whether those polymorphisms are present on the same copy of the gene (i.e., the same chromosome). For example, two polymorphisms could be present on one gene (in which case the two markers are said to be in cis phase), or alternatively the two polymorphisms could be present on different chromosomes (in which case the two markers are said to be in trans phase). Thus, if an individual is heterozygous for particular variants, it is necessary to establish whether both mutations are in cis or in trans to correctly analyze the individual's disease risk status and provide adequate genetic counseling.
Although genetic polymorphisms at a single genetic locus can be easily detected using basic PCR techniques, it is significantly more complex to determine the haplotype of a locus having polymorphisms at multiple genetic loci. Traditionally, haplotyping of multiple mutations has been established by analysis of the parental lineage when available or by inference from genotypes in rare cases of homozygocity or known compound heterozygotes. Such methods, however, are costly and time consuming, and are not therefore practical for use in clinical or diagnostic situations.
A number of alternative approaches have been developed to determine the haplotype or linkage phase of a gene (the particular combination of polymorphisms on a gene) using molecular methods. For haplotyping of a gene with multiple polymorphisms located short distances from each other, the typical approach has been to use allele specific amplification by PCR, a relatively easy method that has generally been useful only for analysis of polymorphisms sufficiently close in proximity that the genetic loci of the polymorphisms can be amplified together (typically in the range of 1 kilobase (kb), the practical limit of accurate PCR amplification) (See, e.g., Ruano et al., Nucleic Acids Res. 1989, 17:8392). Allele specific amplification is commonly used in genotyping assays where both alleles are amplified with distinguishable primers and analyzed.
Wu et al. disclose a direct molecular haplotyping method that uses allele-specific enzymatic PCR amplification of the beta-globin genomic DNA to diagnose sickle cell anemia. Two allele-specific oligonucleotides primers, one specific for the sickle cell allele and one specific for the normal allele, together with another primer complementary to both alleles were used in the polymerase chain reaction with genomic DNA templates. The allele-specific primers differed from each other in their terminal 3′ nucleotide. PCR amplification was performed under annealing temperatures and polymerase chain reaction conditions that permitted directed amplification on their complementary allele. The authors suggest, however, that the DNA polymerase enzyme used to initiate primer extension cannot possess 3′→5′ exonuclease activity, since “such an activity would correct the mismatched base pair in the mismatched primer-template complex and then permit efficient priming with the one-nucleotide-shorter primer”. Thus, the allele-specific PCR amplification of Wu et al. is useful for discriminating between two alleles that differ by a single nucleotide, but this method is useful only when the DNA polymerase lacks 3′→5′ exonuclease activity, since such an enzyme would otherwise remove the single nucleotide mismatch and allow PCR to proceed with both alleles, thereby negating the discriminatory ability of the assay.
For haplotyping of polymorphisms separated by greater distances on a gene, the most common methods have required physical separation of chromosomes or cloning of individual alleles to identify which mutations are present on which of the two diploid chromosomes. These haplotyping technologies are impractical and cost-prohibitive for clinical applications, and have rarely been applied to clinical testing for several reasons: the methods are labor intensive and highly sophisticated, rely on extreme dilution of DNA not practical in a clinical setting, are limited to short fragments of DNA, or are not accurate enough to determine haplotypes from specific individuals.
Recently, a molecular haplotyping technique has been disclosed that uses a two-step procedure to determine the phase of two distantly located alleles (McDonald et al., Pharmacogenetics 2002, 12:93-99). First, long range PCR is used to amplify the region of the gene containing both polymorphic loci, followed by post PCR intramolecular ligation (circularization) to bring the polymorphisms into close proximity so that PCR amplification can be used to determine whether the polymorphisms reside on the same or different chromosomes. This approach has the disadvantage of requiring additional post-PCR steps prior to analysis, and is susceptible to intermolecular ligation between molecules, which can confound results.
Another method for molecular haplotyping of distantly located genetic markers has been disclosed by Michalatos-Beloin et al. (Nucleic Acids Research 1996, 24:4841-4843). In this method, the haplotype of a bi-allelic Alu deletion and a multi-allelic pentanucleotide short tandem repeat (STR) are separated by 10 kb. Both alleles differ by an Alu insertion, providing a long specific sequence for the allele-specific primer. This method requires significant differences between the different alleles at a particular genetic locus, and is not useful for discriminating between alleles that differ by a single nucleotide.
Inbar et al. (Nucl. Acids Res. 30 (15) e76 (2002) disclose determination of haplotypes of two SNPs, SNP888 and SNP988, in close vicinity, separated by a distance of 7.4 kb in the APOE gene, using the method described by Michalatos-Beloin et al., described above.
Advances in the field of human genome mapping, the search for complex disease determinants, pharmacogenomics and accumulation of data from mutation screening programs emphasize the need to develop efficient and cost-effective methods for direct molecular haplotyping, without relying on family pedigree analysis, cloning or complex instrumentation.